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mRNA Transcript Expression in the Ear Shoot Apical Meristem and Correlation with Yield A Translational Genomics Experiment Utilizing Next-Generation Sequencing Technology And the B73 Genome Reference Sequence GENETIC MATERIALS Four homozygous lines: Ex-PVP Accessions Very similar in rate of development (1) LH1 (2) PHG39 (3) LH123HT (4) PHG84 Six F1 Hybrids Six F2 Families Twelve Reciprocal BC1 Families: A*B/A; A*B/B Provides the entries for a generation means design for the partition of genotypic variation into additive, dominance, and inter-gametic epistatic genetic effects EXPERIMENTAL DESIGN Ear Shoot Sampling Ear Trait Phenotyping Ear Trait Phenotyping Ear Shoot Sampling BC1 BC1 F2 F2 Parents Parents F1 F1 Rep 1 BC1’ F1 F2 BC1’ F1 F2 Ear Shoot Sampling Ear Trait Phenotyping Parents Parents F2 F2 Rep 3 BC1’ BC1 F1 BC1’ BC1 F1 Rep 2 Parents BC1’ BC1 Parents BC1’ BC1 • Generations blocked separately so as to eliminate unequal interplot competition effects due to differences in vigor and rate of development. • Ear shoot sampling and ear trait phenoTyping blocked separately so as to provide Normal ear development on intact plants. • Sequencing and bioinformatics done on extracted mRNA by National Center for Genome Resources. TRAIT WEIGHTS ON FIRST PRINCIPAL COMPONENT OF GENOTYPIC VARIATION IN THE MATURE EAR 0.50 First principal component accounts for 90% of the variation in ear traits Variation primarily Non-additive 0.40 0.30 0.20 0.10 Kernels Per Row Grain Weight Ear Weight Grain Fill Cob Length Cob Weight 18,000 FREQUENCY DISTRIBUTION OF TRANSCRIPT EXPRESSION GENETIC EFFECTS AT FDR<=0.10 15,000 12,000 9,000 6,000 3,000 Genotypic Additive Dominance InterGametic Epistatic Residual Genetic PERCENT OVER-REPRESENTATION OF GENES WITH TRANSCRIPT EXPRESSION SIGNIFICANTLY CORRELATED WITH KPR COMPONENT BY FUNCTIONAL CATEGORY 60 50 40 30 20 10 OxidoReductase Transcription Factors Heat Shock Stress Response All Others RANK CORRELATIONS OF GENE EXPRESSION WITH KERNELS PER ROW COMPONENT CCAAT cAMP Enhancer Binding Protein Responsive Element Binding C/EBP CREB 1.0 0.5 0 -0.5 -1.0 Ramosa1 Ramosa2 Ramosa3 Ramosa3 Chr 2 Chr 7 Homeolog Ramosa 1 Ramosa2 Ramosa3 homeolog Knox 1 ELK Pyruvate dehydrogenase Transketolase Tubby C/EBP N=394 Biosynthesis r>=0.82 r=1 Kernels per row r 1 CREB Superoxide dismutase Detox proteins (several) Haem peroxidases (several) NADH plastoquinone Iron-sulfur protein AMP-dependent synthetase Adenine translocator AP2/EREPB r=-1 r<=-0.82 N=451 Generation of Reactive Oxygen Species (ROS) DueTo OxidoReductase Activity During Mitochondrial Respiration SUMMARY • Variation in genotypic expression of the ramosa genes in the ear shoot spikeletpair meristem is highly correlated with genotypic variation in kernels per row in the mature ear. • Reactive oxygen species may serve as a signal acting on a gene network centered on C/EBP and CREB that regulates initiation of axillary branches in the spikelet-pair meristem. ACKNOWLEGEMENTS Andrew Farmer NCGR Paul Scott Iowa State Bill Beavis Iowa State Bob Schmidt UCSD Sarah Hake & Maize Infl. Group Adrienne Lauter Iowa State Greg May NCGR Kendall Lamkey Iowa State QUESTIONS & COMMENTS ?